In this season, the team deals with the aftermath of an explosion that results in a casualty connected to the agency. Tony travels to Israel on the search for missing Ziva, and Gibbs and McGee head to Afghanistan to solve a murder.
Season 3 opens with Kara dealing with the loss on Mon-El by focusing her energy on being Supergirl and concentrating on a mysterious new threat; Alex confessing a secret to Maggie; a citizen of National City having a mysterious connection to Kara; Lena making a bold move.
After the Battle of New York, the world has changed. It now knows not only about the Avengers, but also the powerful menaces that require those superheroes and more to face them. In response, Phil Coulson of the Strategic Homeland Intervention, Enforcement and Logistics Division assembles an elite covert team to find and deal with these threats wherever they are found. With a world rapidly becoming more bizarre and dangerous than ever before as the supervillains arise, these agents of S.H.I.E.L.D. are ready to take them on.